Merge pull request #382 from broadinstitute/ami-FixBcfCoder-52571227

Ami fix bcf coder 52571227

public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java

@@ -75,7 +75,7 @@ public class GATKVCFUtils {
         attributes.put("Date", date.toString());
         attributes.put("Epoch", Long.toString(date.getTime()));
         attributes.put("CommandLineOptions", engine.createApproximateCommandLineArgumentString(argumentSources.toArray()));
-        return new VCFSimpleHeaderLine(GATK_COMMAND_LINE_KEY, attributes, Collections.<String>emptyList());
+        return new VCFSimpleHeaderLine(GATK_COMMAND_LINE_KEY, attributes);
     }
 
     public static <T extends Feature> Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, List<RodBinding<T>> rodBindings) {

settings/repository/net.sf/picard-1.96.1534.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.96.1525" status="release" />
+    <info organisation="net.sf" module="picard" revision="1.96.1534" status="release" />
 </ivy-module>

settings/repository/net.sf/sam-1.96.1525.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.96.1525" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.96.1534.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.96.1534" status="release" />
+</ivy-module>

settings/repository/org.broad/tribble-1.96.1534.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="1.96.1526" status="integration" />
+    <info organisation="org.broad" module="tribble" revision="1.96.1534" status="integration" />
 </ivy-module>

settings/repository/org.broadinstitute/variant-1.96.1534.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="variant" revision="1.96.1525" status="integration" />
+    <info organisation="org.broadinstitute" module="variant" revision="1.96.1534" status="integration" />
 </ivy-module>